Difference between revisions of "Team:Cambridge-JIC/Attributions"

 
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<h1 style="line-height:1.295em"> Attributions </h1>
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<center><h1 style="line-height:1.295em"> Attributions </h1></center>
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<center><p><i>We would like to thank our supervisor, advisors, and the many people who have generously shared their time and expertise with us, and without whom this project would not have been possible, let alone finished in time…</i></p></center>
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<h3>Special thanks to:</h3>
 
<h3>Special thanks to:</h3>
<p><i>We would like to thank our supervisor, advisors, and the many people who have generously shared their time and expertise with us, and without whom this project would not have been possible, let alone finished in time…</i></p>
+
<p><b>Dr Richard Bowman</b>, NanoPhotonics Center, University of Cambridge<br>
<p><b>Dr Richard Bowman</b> [NanoPhotonics Center, University of Cambridge]<br>
+
For inspiring our entire project, and providing the basis for our microscope stage with his PiScope (an open-source, inverted, bright-field microscope). See <a href="http://arxiv.org/abs/1509.05394" class="blue">here</a> for more information about PiScope [1].</p>
For inspiring our entire project, and providing the basis for our microscope stage with his PiScope (an open-source, inverted, bright-field microscope). Click <a href="" class="blue">here</a> for more information about PiScope.</p>
+
<p><b>Prof Jim Haseloff</b>, Department of Plant Sciences, University of Cambridge<br>  
<p><b>Prof Jim Hasseloff</b> [Department of Plant Sciences, University of Cambridge]<br>  
+
 
For his support and patience as our PI. Particularly for organising consultation meetings, logistics and helping at every step of the way.</p>
 
For his support and patience as our PI. Particularly for organising consultation meetings, logistics and helping at every step of the way.</p>
<p>In terms of <span class="hl_2">safety and wellbeing</span>, infinite credit to <span class="hl_2">Kate Armfield</span>, our wonderful full-time advisor, who has helped us in all aspects of our project, including <span class="hl_2">logistics</span>, <span class="hl_1">press releases</span> and generally making sure we don’t set things on fire. Also thanks to <span class="hl_2">Barbara Landamore</span>, chief technician extraordinaire, who helped us with <span class="hl_2">risk assessments and lab protocols</span> and not chopping our hands off.</p>
+
<p><b>Kate Armfield</b>, PhD student, University of Glasgow<br>
<p>On the <span class="hl_1">optical design</span> front, we would like to thank <span class="hl_1">Dr George Sirinakis</span> and <span class="hl_1">Dr Alex Sossick</span> from the Gurdon institute, who gave us advice on how to improve the performance of our microscope. Credit is also due to <span class="hl_1">Tobey Wenzel</span> and <span class="hl_1">Luka Mustafa</span> for their help with <span class="hl_1">electronics and other hardware</span> aspects of our project.</p>
+
For being a wonderful full-time advisor, who has helped us in all aspects of our project, including logistics, press releases and lab supervision.</p>
<p>During the very <span class="hl_2">early brainstorming</span> stage of our project, we had expert help from several people. In particular, thanks to <span class="hl_2">Bernardo Pollak</span> for his help with <span class="hl_2">Marchantia</span>, <span class="hl_2">Dr Dennis Bray</span> for his talk on <span class="hl_2">bacterial chemotaxis</span> and <span class="hl_2">Dr James Locke</span> for his contribution to the <span class="hl_2">Evolvinator</span> idea. And of course, <span class="hl_2">Dr Bowman</span>, who showed us his <span class="hl_2">PiScope</span> in action.</p>
+
<p><b>Barbara Landamore</b>, Department of Plant Sciences, University of Cambridge<br>
<p>We are grateful to <span class="hl_1">Dr Nicola Patron</span> and others at the John Innes Centre, for supporting our project and giving us <span class="hl_1">feedback</span> on our preliminary presentation and on the microscope itself. Thanks also to <span class="hl_1">Dr Jenny Molloy</span> for organising a practice Jamboree <span class="hl_1">presentation</span> for us, and for giving us advice on a regular basis, and to <span class="hl_1">Dr Alexandre Kabla</span> from the Department of Engineering, for <span class="hl_1">project advice</span> and for convincing the Engineering Department to give us a lot of <span class="hl_1">money</span> (yay!).</p>
+
For helping with risk assessments and lab protocols, and sourcing key materials.</p>
<p>In terms of <span class="hl_2">collaboration</span>, thanks to the <span class="hl_2">Glasgow and William & Mary iGEM teams</span> for sending us some samples to image (and to <span class="hl_2">Dr Paul Grant</span> for helping us with some <span class="hl_2">bacteria transformations</span>), and to the <span class="hl_2">Westminster iGEM team</span> for helping us organise a microscopy workshop at their <span class="hl_2">UK iGEM meetup</span>.</p>
+
<p><b>Dr George Sirinakis</b> and <b>Dr Alex Sossick</b>, Gurdon Institute, University of Cambridge<br>
<p>We are also indebted to <span class="hl_1">Sarah Collins</span>, <span class="hl_1">Tom Almeroth-Williams</span>, <span class="hl_1">Sue Long</span>, and <span class="hl_1">Louise Walsh</span> from Cambridge University Press for helping with our <span class="hl_1">press releases</span> and our <span class="hl_1">outreach</span> event.</p>
+
For their advice on how to improve the optical performance of our microscope.</p>
<p>Thanks to <span class="hl_2">Amanda Whitehead</span> and <span class="hl_2">Dr Shaila Kotadia</span> from Synthetic Dance-ology, for picking our microscope as the focus of their <span class="hl_2">dance workshop</span>; <span class="hl_2">Prof Clemens Kaminski</span> of the Laser Analytics Group for his stimulating talk on <span class="hl_2">Optical Superresolution Imaging</span> at Homerton College; and last by not least, <span class="hl_2">Dr Fernán Federici</span>, <span class="hl_2">Dr James Brown</span> and all the other people who have encouraged us and given us <span class="hl_2">feedback</span>.</p>
+
<p><b>Prof. Dale Sanders</b>, Head of the John Innes Centre, and <b>Prof. Duncan Maskell</b>, Head of the School of Biological Sciences, University of Cambridge<br> For enthusiastic leadership and generous support.</p>
 +
<p><b>BBSRC/EPSRC OpenPlant Synthetic Biology Research Centre</b><br> For funding support.</p>
 +
<p><b>Tobias Wenzel</b>, Department of Physics, University of Cambridge<br>
 +
For his constant guidance with optical pathway design and illumination.</p>
 +
<p><b>Luka Mustafa</b>, Shuttleworth Fellow, IRNAS<br>
 +
For his appraisal of our hardware design and advice on custom PCBs.</p>
 +
<p><b>Bernardo Pollak</b>, Department of Plant Sciences, University of Cambridge<br>
 +
For his assistance with samples for imaging, and advice about <i>Marchantia</i>.</p>
 +
<br>
 +
<p style="font-size:80%">[1] Sharkey, J., Foo, D., Kabla, A., Baumberg, J. and Bowman, R. (2015). <i>A one-piece 3D printed microscope and flexure translation stage.</i><a href="http://arxiv.org/abs/1509.05394" class="blue">[online]</a> Arxiv.org. [Accessed 18 Sep. 2015].</p>
 
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<h3 style="line-height:1.295em"> Teamwork </h3>
+
<h3>Thanks also to:</h3>
 +
<p><b>Professor Emeritus Dennis Bray</b>, Department of Physiology, Development and Neuroscience, University of Cambridge<br>
 +
For his talk on bacterial chemotaxis.</p>
 +
<p><b>Dr James Locke</b>, Sainsbury Laboratory, University of Cambridge<br>
 +
For his advice on the Evolvinator concept.</p>
 +
<p><b>Dr Nicola Patron</b>, The Sainsbury Laboratory, Norwich<br>
 +
For her feedback on our presentation and microscope at a visit day in Norwich that she helped organise. </p>
 +
<p><b>Dr Jenny Molloy</b>, Department of Plant Sciences, University of Cambridge<br>
 +
For her feedback on our Human Practices project.</p>
 +
<p><b>Dr Alexandre Kabla</b>, Department of Engineering, University of Cambridge<br>
 +
For assisting with funding, courtesy of the Department of Engineering. </p>
 +
<p><b>Dr Jim Ajioka</b>, University of Cambridge<br> For his mentorship and help in Cambridge.</p>
 +
<p><b>Professor George Lomonossoff</b><br> For coordination with the John Innes Centre.</p>
 +
<p><b>Dr Pietro Cicuta</b> Physics Department, University of Cambridge<br> For support in the Physics Department.</p>
 +
<p><b>Dr Paul Grant</b>, Department of Plant Sciences, University of Cambridge<br>
 +
For supervision in the laboratory and guiding us through transformations.</p>
 +
<p><b>Sarah Collins</b>, <b>Dr Tom Almeroth-Williams</b>, <b>Sue Long</b> and <b>Dr Louise Walsh</b>, Cambridge University Press<br>
 +
For helping with our press releases and our outreach event.</p>
 +
<p><b>Amanda Whitehead</b> and <b>Dr Shaila Kotadia</b>, Synthetic Dance-ology<br>
 +
For picking our microscope as the focus of their dance workshop.</p>
 +
<p><b>Prof Clemens Kaminski</b>, Laser Analytics Group, University of Cambridge<br>
 +
For his stimulating talk on Optical Superresolution Imaging.</p>
 +
<p><b>Dr Tim Weil</b>, Department of Zoology, University of Cambridge<br>
 +
For his incredible help in providing samples for our outreach day.</p>
 +
<p><b>Dr Fernán Federici</b>, <b>Dr James Brown</b> and all the other people who have encouraged us and given us feedback.</p>
 +
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<h3>In terms of collaboration, thanks to:</h3>
 +
<p><b>Glasgow</b> and <b>William & Mary iGEM teams</b><br>
 +
For sending us some samples to image.</p>
 +
<p><b>The Westminster iGEM team</b><br>
 +
For helping us organise a microscopy workshop at their UK iGEM meetup.</p>
 
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<h3>Teamwork</h3>
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<h4><center>Mechanical Design</center></h4>
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<p><center>Simon, Katerina</center></p>
 +
</div>
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<div class="factcol" style="background-color:#bde9fe;color:#123a68">
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<h4><center>Optical Design</center></h4>
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<p><center>Simon, Katerina, Ocean</center></p>
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<h4><center>Electronics and Hardware</center></h4>
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<p><center>Souradip, Rajiv, Simon</center></p></div>
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<div class="factcol"  style="background-color:#b1e7ad;color:#1b4f18">
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<h4><center>Software</center></h4>
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<p><center>Will, Souradip, Ocean, Rajiv</center></p>
 +
</div>
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<div class="factcol" style="background-color:#bde9fe;color:#123a68">
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<h4><center>Human Practices</center></h4>
 +
<p><center>Atti</center></p>
 +
</div>
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</div>
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<div class="factcol-container">
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<div class="factcol" style="background-color:#c6b2e4;color:#4c366e">
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<h4><center>Outreach</center></h4>
 +
<p><center>Ocean, Olivia, María, Will</center></p></div>
 +
<div class="factcol"  style="background-color:#b1e7ad;color:#1b4f18">
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<h4><center>Wiki</center></h4>
 +
<p><center>Will, Souradip, Simon, Katerina, Atti, Lorenzo</center></p>
 +
</div>
 +
<div class="factcol" style="background-color:#bde9fe;color:#123a68">
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<h4><center>Graphics Design</center></h4>
 +
<p><center>Simon, Ocean, Olivia</center></p>
 +
</div>
 +
<div class="factcol" style="background-color:#c6b2e4;color:#4c366e">
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<h4><center>Documentation</center></h4>
 +
<p><center>Atti, Souradip, Simon, María, Katerina</center></p></div>
 +
<div class="factcol"  style="background-color:#b1e7ad;color:#1b4f18">
 +
<h4><center>Sponsorship</center></h4>
 +
<p><center>Lorenzo, Atti, María</center></p>
 +
</div>
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 +
<h2>Open Source Projects</h2>
 +
<h3>Software</h3>
 +
<p>Below is a list of software programs that we have found useful for developing open-source documentation, supplemented with other commonly used programs:</p>
 +
<ol>
 +
<li><p>OpenSCAD – a free, open-source, parametric CAD platform used to design 3D objects for printing (available from <a href="http://www.openscad.org" class="blue">here</a>)</p></li>
 +
<li><p>Tracker – a free, open-source, video analysis and modelling tool. Used to track moving objects in videos and extract data (available from <a href="http://physlets.org/tracker/" class="blue">here</a>)</p></li>
 +
<li><p>Cura 3D – a free, open-source 3D printer interface from Ultimaker. Used to control printer settings (available from <a href="https://ultimaker.com/en/products/cura-software" class="blue">here</a>)</p></li>
 +
<li><p>Fiji - a free, open-source image processing and analysis platform. Particularly useful for microscopy (available from <a href="http://fiji.sc/Fiji" class="blue">here</a>)</p></li>
 +
<li><p>Inkscape – a free, open-source vector graphics package. Extremely useful for 2D design followed by linear extrusion (available from <a href="https://inkscape.org/en/" class="blue">here</a>)</p></li>
 +
<li><p>DesignSpark – a free electronics design software for PCB prototyping. Has an online library of over 80,000 parts (available from <a href="http://www.rs-online.com/desig-nspark/electronics/" class="blue">here</a>)</p></li>
 +
<li><p>Scribus – a free, open-source graphics software. Particularly useful for publishing (available from <a href="http://www.scribus.net/" class="blue">here</a>)</p></li>
 +
 +
<li><p>Python – a free, open-source, programming language that allowed us to put together software quickly</p></li>
 +
<li><p>Nginx – A FOSS lightweight web server on top of which we built our web interfaces.</p></li>
 +
<li><p>OpenCV – A FOSS released under a BSD license that provides a library for image processing software (available from <a href="http://opencv.org/" class="blue">here</a>)</p></li>
 +
</ol>
 +
<p>For a detailed list of free, open-source software programs available, look <a href="http://www.datamation.com/open-source/open-source-software-list-2015-ultimate-list-1.html" class="blue">here</a>.</p><br>
 +
<h3>Hardware</h3>
 +
<ol>
 +
<li><p>Arduino – A low-cost, open-source microprocessor with a number of available add-ons. Includes its own specific programming software and language (available <a href="https://www.arduino.cc/" class="blue">here</a>).</p></li>
 +
<li><p>Raspberry Pi – A low-cost, linux-based computer board with a wide range of compatible modules including cameras and Wi-Fi adapters (available <a href="https://www.raspberrypi.org/" class="blue">here</a>).</p></li>
 +
</ol>
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Latest revision as of 15:02, 18 September 2015

Attributions


We would like to thank our supervisor, advisors, and the many people who have generously shared their time and expertise with us, and without whom this project would not have been possible, let alone finished in time…


Special thanks to:

Dr Richard Bowman, NanoPhotonics Center, University of Cambridge
For inspiring our entire project, and providing the basis for our microscope stage with his PiScope (an open-source, inverted, bright-field microscope). See here for more information about PiScope [1].

Prof Jim Haseloff, Department of Plant Sciences, University of Cambridge
For his support and patience as our PI. Particularly for organising consultation meetings, logistics and helping at every step of the way.

Kate Armfield, PhD student, University of Glasgow
For being a wonderful full-time advisor, who has helped us in all aspects of our project, including logistics, press releases and lab supervision.

Barbara Landamore, Department of Plant Sciences, University of Cambridge
For helping with risk assessments and lab protocols, and sourcing key materials.

Dr George Sirinakis and Dr Alex Sossick, Gurdon Institute, University of Cambridge
For their advice on how to improve the optical performance of our microscope.

Prof. Dale Sanders, Head of the John Innes Centre, and Prof. Duncan Maskell, Head of the School of Biological Sciences, University of Cambridge
For enthusiastic leadership and generous support.

BBSRC/EPSRC OpenPlant Synthetic Biology Research Centre
For funding support.

Tobias Wenzel, Department of Physics, University of Cambridge
For his constant guidance with optical pathway design and illumination.

Luka Mustafa, Shuttleworth Fellow, IRNAS
For his appraisal of our hardware design and advice on custom PCBs.

Bernardo Pollak, Department of Plant Sciences, University of Cambridge
For his assistance with samples for imaging, and advice about Marchantia.


[1] Sharkey, J., Foo, D., Kabla, A., Baumberg, J. and Bowman, R. (2015). A one-piece 3D printed microscope and flexure translation stage.[online] Arxiv.org. [Accessed 18 Sep. 2015].

Thanks also to:

Professor Emeritus Dennis Bray, Department of Physiology, Development and Neuroscience, University of Cambridge
For his talk on bacterial chemotaxis.

Dr James Locke, Sainsbury Laboratory, University of Cambridge
For his advice on the Evolvinator concept.

Dr Nicola Patron, The Sainsbury Laboratory, Norwich
For her feedback on our presentation and microscope at a visit day in Norwich that she helped organise.

Dr Jenny Molloy, Department of Plant Sciences, University of Cambridge
For her feedback on our Human Practices project.

Dr Alexandre Kabla, Department of Engineering, University of Cambridge
For assisting with funding, courtesy of the Department of Engineering.

Dr Jim Ajioka, University of Cambridge
For his mentorship and help in Cambridge.

Professor George Lomonossoff
For coordination with the John Innes Centre.

Dr Pietro Cicuta Physics Department, University of Cambridge
For support in the Physics Department.

Dr Paul Grant, Department of Plant Sciences, University of Cambridge
For supervision in the laboratory and guiding us through transformations.

Sarah Collins, Dr Tom Almeroth-Williams, Sue Long and Dr Louise Walsh, Cambridge University Press
For helping with our press releases and our outreach event.

Amanda Whitehead and Dr Shaila Kotadia, Synthetic Dance-ology
For picking our microscope as the focus of their dance workshop.

Prof Clemens Kaminski, Laser Analytics Group, University of Cambridge
For his stimulating talk on Optical Superresolution Imaging.

Dr Tim Weil, Department of Zoology, University of Cambridge
For his incredible help in providing samples for our outreach day.

Dr Fernán Federici, Dr James Brown and all the other people who have encouraged us and given us feedback.

In terms of collaboration, thanks to:

Glasgow and William & Mary iGEM teams
For sending us some samples to image.

The Westminster iGEM team
For helping us organise a microscopy workshop at their UK iGEM meetup.

Teamwork

Mechanical Design

Simon, Katerina

Optical Design

Simon, Katerina, Ocean

Electronics and Hardware

Souradip, Rajiv, Simon

Software

Will, Souradip, Ocean, Rajiv

Human Practices

Atti

Outreach

Ocean, Olivia, María, Will

Wiki

Will, Souradip, Simon, Katerina, Atti, Lorenzo

Graphics Design

Simon, Ocean, Olivia

Documentation

Atti, Souradip, Simon, María, Katerina

Sponsorship

Lorenzo, Atti, María


Open Source Projects

Software

Below is a list of software programs that we have found useful for developing open-source documentation, supplemented with other commonly used programs:

  1. OpenSCAD – a free, open-source, parametric CAD platform used to design 3D objects for printing (available from here)

  2. Tracker – a free, open-source, video analysis and modelling tool. Used to track moving objects in videos and extract data (available from here)

  3. Cura 3D – a free, open-source 3D printer interface from Ultimaker. Used to control printer settings (available from here)

  4. Fiji - a free, open-source image processing and analysis platform. Particularly useful for microscopy (available from here)

  5. Inkscape – a free, open-source vector graphics package. Extremely useful for 2D design followed by linear extrusion (available from here)

  6. DesignSpark – a free electronics design software for PCB prototyping. Has an online library of over 80,000 parts (available from here)

  7. Scribus – a free, open-source graphics software. Particularly useful for publishing (available from here)

  8. Python – a free, open-source, programming language that allowed us to put together software quickly

  9. Nginx – A FOSS lightweight web server on top of which we built our web interfaces.

  10. OpenCV – A FOSS released under a BSD license that provides a library for image processing software (available from here)

For a detailed list of free, open-source software programs available, look here.


Hardware

  1. Arduino – A low-cost, open-source microprocessor with a number of available add-ons. Includes its own specific programming software and language (available here).

  2. Raspberry Pi – A low-cost, linux-based computer board with a wide range of compatible modules including cameras and Wi-Fi adapters (available here).